Mass Effect 4: The Ninja Alliance
by Rex Resede90
Summary: Just when all hope fades for the Council Species, a new and mysterious fleet arrives from beyond their galaxy. Calling themselves the Ninja Alliance, they quickly show that they can take on the Reapers, but will it be enough? Or will the cycle of genocide continue? A Mass Effect/Star Wars/Star Trek crossover.


Mass Effect

Fall of the Reapers

Chapter 1: Arrival of the Alliance

**Hiya gang! Names Rex Resede90, a Lance Corporal serving in the United States Marine Corps, and this is my first story that I'm writing. It'll be based in the Mass Effect universe, after the end of ME3. In this version, the Crucible failed to work on the Reapers, and the Citadel Fleet is on the run, much like the Colonials in Battlestar Galactica. However, just when things look bleak for their survival, they receive a surprise in the form of my group of OCs, the Ninja Alliance, and no, the Naruto characters will NOT be in here. My Ocs will be using ships from famous movies like Star Wars and Star Trek.**

**Disclaimer: I do not own Mass Effect, Star Wars, or any other Sci-Fi object in existence. If I did, this would be how it would go, and Shepard wouldn't have had to be sacrificed to beat the Reapers.**

The war against the Reapers wasn't going well for the Citadel Council and its members at all. Ever since the failed attempt to retake Earth, where the combined forces of the entire galaxy lost almost 75% of their military and the Crucible failed to work on the Reapers, what remained of the fleet had separated into smaller groups and scattered, on the run, barely staying one step ahead of the seemly invincible enemy. One of those fleets was currently sitting in orbit of the planet Ilos, in the Pangaea Expanse. The Council came here to look for a way, any way, to survive what they were coming to see as their extinction, and they were searching for the Prothean AI, Vigil, who they hoped might have an answer for them. The problem is that the Reapers could appear at any time, and they weren't sure if they could escape this time.

_Surface of Ilos _

At the entrance to the ruins where they first met Vigil and learned of the Reapers' power, Commander Alexender Shepard and his team were preparing to enter the ruins to see Vigil, and find out if there was a way to hide from the Reapers til they could recover their strength and take the fight back to the damn machines. As he looked around at the faces of all his friends, Alex couldn't help but notice just badly their hope for the future had been shattered. Off to his left, Ashley Williams, James Vega, Zaeed Massani, and Kasumi Goto were talking about the chances of their own survival in what was sure to come. To his right, EDI, Jack, Thane Krios, Miranda Lawson, Jacob Taylor and Legion were doing a weapons count, checking how many thermal clips they had left. Little ways down from them, Samara, Grunt and Javik were talking about just how many of the bastards they were planning to take down with them, should it come to that. And out of sight of everyone, Liara T'Soni was clutched in Garrus Vakarian's arms, silent tears falling from her eyes as she continued to try to think of way for them to survive the coming storm. And as he looked around, he also couldn't help but notice that one person wasn't down here with them, his fiancee, Tali'Zorah vas Normandy, who was still up on the _**Normandy**_, still badly injured and possibly dying from Harbinger's last attack, which would have killed him had she not pushed him out of the way.

Just thinking about her current state nearly broke him, and Shepard knew, in his heart, if she died, he wasn't gonna be far behind her. But as he continued to think about Tali's state, he felt a hand being placed on his shoulder. Looking behind him, he saw that Garrus had come up behind him, looking at him in concern.

"You ok, Shepard?"

"Yes. . . . . No. Its just, all the blood we've shed trying to stop the Reapers, all the heartache we went through trying to build the Crucible, and yet we failed, I failed, to stop them, to protect everyone. Now we're on the run, fighting to survive, the Reapers are stronger than ever, the woman I love is possibly dying, and I'm stuck down here, trying to find a way for all of us to escape what is possibly our fate." Alex said, looking at the turian that he had come to consider as a brother in all but blood.

Garrus took the opportunity to get a good long look at Shepard, noting the obvious signs of exhaustion and frustration, but also noticing something else that no one else who didn't know the man as well as he did: Despair. And he knew why, too. With Tali in a coma that Chakwas, their doctor, had no idea if she would survive long enough to _come out _of, much less recover from, due to her injuries. If she died, Shepard would be devastated beyond any chance of recovery.

'_Tali, you better wake up soon, because I don't think Shepard can go on without you there with him._' he thought to himself, praying to any and every deity he could think of for the miracle that they all needed to bring back the one thing they were slowly losing: Hope. . . . .

_Han System, Gemini Sigma_

In the Han System, a strange event had started to occur near the edge of the system. One moment, there was nothing. The next, an explosion, followed by the formation of a _massive _wormhole in space. From the wormhole, another strange event occurred: a small group of triangular starships poured from the event, in a standard recon formation. As soon as the ships cleared the wormhole, it suddenly closed, followed by another, smaller explosion. The small recon fleet, numbering one 19 kilometer long dreadnought, three 1.6 kilometer cruisers, and five 752 meter frigates. The ships then started releasing small fighters that started to patrol the area around the group as they moved through the system. On board the dreadnought's bridge, the command crew were busy working, scanning every square inch of the system, searching for their elusive foes, the machines that had engaged their fleet back in their home in the farthest reaches of darkspace, known to them as the Forbidden Zone. The problem was that this galaxy had an entire civilization living here in this galaxy, and they were being attacked by the machines.

_On Board The Executor-class Super Star Destroyer __**Demonslayer**_

"Captain, our sensors have picked up signs that our _old_ friends are here and have engaged what looks like an advanced civilization. The situation, though, is much worse than the Council of Ninjas feared, sir." Petty Officer Lisa Derrow reported, after reviewing what their sensors showed.

"How bad are we talking, Derrow?" asked the captain, Captain Alzerath Winters, as he continued to look out the viewport, watching as the fleet continued to fly through space in formation. Several TIE Interceptors then flew by in tight formation as they performed their duty as sentries for the fleet. The captain had been one of several who volunteered to fly out into the universe to track down the beings that call themselves the Reapers.

Lisa looked up at the captain to give him the news, "The Reapers' weapons, shields, and armor are many times more advanced than this civilization's technology. Hell, their tech seems based off of the Reapers, only much too inferior to be at all that effective against them. It's only a matter of time before this 'Citadel Council' is wiped out. Of course, that's only if we don't interfere with this 'cycle'."

Captain Winters continued to watch the fleet, before turning and walking down the aisle til he got to his command chair. As he sat down, he looked to his pilot and was about to tell him to start the countdown for hyperspace, when his communications officer, Lt David Cyfer, started to yell at the top of his lungs.

"SIR! I'm picking up an emergency distress call coming from the Pangaea Expanse. The Reapers have found what remains of the Citadel Fleet and engaged them. They're taking heavy casualties and they have civilians that they are trying to protect. They are in need of assistance!"

"Then what the hell are we waiting for? Helm, set course for the Pangaea Expanse, all power to the hyperdrive! Sound Battlestations, recall our fighters and let the other ships know what's going on."

"YES SIR!" the entire bridge crew sounded off, as they rushed to their stations to prepare for battle. As one, all eight ships engaged their hyperdrives and disappeared from sight as they entered hyperspace.

_Pangaea Expanse, Ilos Orbit_

Things had gone from bad to worse in the span of a few hours. After finding out that Vigil had indeed disappeared, Shepard and the others had returned to the **_Normandy_**, only to learn that the Reapers had found them and trapped them in the system. What followed after that was an hour of destruction, as the Reapers basically started to target and destroy the ships, with three of them keeping the civilian ships from leaving the area. Unfortunately, that still left just over thirty warships of varying classes up against ten _Sovereign_-class Reapers, which were not good odds to begin with as three could easily destroy twice that number before losing even one of their number. Even Joker was having a hard time dodging the weapons fire that was flying everywhere, even as a Reaper blasted one of the few Turian dreadnoughts they had left.

"God damn! Can we go anywhere without these guys dropping in on us, or is that too much to ask for!" Joker exclaimed as he pulled yet another crazy maneuver, avoiding two more Reapers and their Oculi fighters before shooting down four of the fighters with the GARDIAN lasers, then firing the last of the disrupter torpedoes at another swarm of fighters.

"Just focus on keeping us alive long enough for EDI to hack the relay so we can get everyone out of here, especially the civilians. EDI, how much longer?" Shepard asked, watching as the small fleet that he had been placed in command of continued to stay alive for as long as possible. '_Come on, baby, stay together, just long enough for us to escape._'

"Shepard, I can't hack the relay, the Reapers' cyber defenses are too strong. And the fleet won't last much longer, the Reapers are too many." EDI said, completely focused on keeping the ship as intact as possible. But as the battle continued, she started to pick up something strange on the long-range sensor nets that they had sent up when they arrived, something strange. According to the sensors, eight unknown ships were fast approaching their position, and just from the readings she was getting, all the ships were giving off the same power levels as the Reaper forces, all except for one ship, which was giving off more then _three times_ the power that the Reapers' mass effect cores provided! She then turned toward Shepard to tell him what she was detecting.

"Commander, long-range sensors have picked up eight unidentified ships on approach. They are giving off the same level of power that the Reapers' cores give off."

Alex looked at her in shock at the news, even as Ashley started questioning EDI. "There's no way that ain't Reaper reinforcements. They have control of the Relay, so how could they be help for us?"

That was when she dropped the bomb on all of them. "I never said they were coming through the Relay."

Before Ash and Alex could question her further, their short-range sensors immediately picked up a massive increase in radiation. . . . . right as eight triangular-shaped warships popped out of nowhere, approaching the battle in a wedge formation. From what they could see, there were five cruisers, two dreadnoughts. . . . . and one massive, 19 kilometer ship! Even as they watched in awe of the mysterious ships, EDI detected the launch of literally _hundreds _of what looked liked starfighters from their hangers, which were located both on the sides and the bottom of the ships.

"HOLY SHIT! Who the hell are these guys?! I mean, GODDAMN, that's some hardware they are packing!" Garrus exclaimed, looking at the group of ships in shock.

"Shepard, I am detecting something. . . . They seem to be hailing the Reapers." EDI said, surprised at what these strangers were doing, and she wasn't the only one.

"WHAT?! Are they loco? Why would they even try?!" Vega shouted out in anger.

"Hold that thought. EDI, can you patch us in, so we can hear what they are saying?" Shepard asked, staring out at the Reapers, who had all stopped the attack and turned around to face the ships. '_What are the_y _doing? It's almost like the Reapers know these guys. . ._'

"Shepard, we are in. Opening comms to the whole fleet."

**_'Reaper forces, this is Ninja Alliance Recon Fleet Delta, Captain Winters of the NAV Super Star Destroyer Demonslayer, calling to all Reaper forces in the area. By order of the Council of Ninjas, you are ordered to stop all attacks and vacant the Milky Way Galaxy immediately. Failure to do so WILL result in the destruction of your fleets that are here.'_**

**_'Rudimentary creatures of flesh and blood, do you believe that you can stop that which cannot be broken? Our fleets are infinite, our strength is eternal, you will not break the cycle that we have performed throughout the universe. You will also pay for the destruction of our fleet that was sent to destroy you and your fleet. You bring chaos and I will be the one to reimpose order through your destruction. I am Tyrant.'_ **

_Pangaea Expanse, Ilos orbit, Bridge of the Demonslayer_

Captain Winters watched as the Reapers, save the three that were near what looked like civilian ships, moved into position to attack them, when he heard his XO, Commander John Dresden, speak up, "Boy, somebody's sounds confidant that he can take us on. Should we tell him what happened to the last bunch that said that?"

Winters looked at his long-time friend, Dresden having been there for him since the Academy back home, before replying to his friend's humor, "Well, what should I say to him, 'Sorry, but we wiped all of your buddies out already, better luck next time?'"

The Commander just shrugged, before looking out at the seven Reapers that were approaching them. "Can't say that, we haven't killed Harbinger yet. That being said, I believe that we now know where the last of these bastards are, so I will contact the Council, while you get the fun job of handling these punks."

"Gee, thanks. Nice to know that I have such a good XO for a friend."

When he looked back at the Reapers that were approaching them, he saw that the bastards were only sending all their fighters and three _Sovereign_-classes at them. '_D__id they actually just do that?_' "Shields up, power up all turbolasers batteries and tell the TIE fighters to engage their Oculis. Have the _Acclamator, Resolute, Liberty, Omega, _and _Endor _target those Reapers that are preventing the civilian ships from escaping while us, the _Longbow, _and the _Imperial _take these suckers and the other four head-on!"

With those commands, the recon fleet moved into action, the five _Acclamator_ II-class frigates jumping into Hyperspace, reappearing seconds later near the civilian ships, taking the three Reapers by surprise as they immediately opened fire on them with their turbolasers. While this was happening, the _Imperator-_class and _Longbow_-classStar Destroyers also jumped, this time targeting the four Reapers that still attacking the badly outmatched military ships, appearing in front of the badly damaged fleet and introducing the Reapers to a devastating broadside, complete with turbolasers, ion cannons, and proton torpedoes, and the _Demonslayer_ and TIE fighters attacked the remaining Reapers and the Oculi fighters. The Reapers were about to learn an very important lesson: the Ninja Alliance wasn't a force to be underestimated!

**So what do you think? Make sure to review plenty and hit me with SOME criticism. Any flames WILL result in a Super Star Destroyer blasting you into orbit! **


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